Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_374 ID=scaffold_374-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8204
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.30
Warning! 464 characters in sequence are not A, C, G, or T
Found at i:1137 original size:44 final size:43
Alignment explanation
Indices: 1077--1231 Score: 148
Period size: 44 Copynumber: 3.5 Consensus size: 43
1067 CCACTTCGCT
* * * * *
1077 ACCAATATAGGAAGACAGGACCTACTATCTTTGATCTACTTCAC
1 ACCAGTATAGGAAGACAAGATCTA-TTTCTTTGATCTACTCCAC
* * * * *
1121 ACCAGTATATGAAGACACGATCTGTTTTCTTCGACCTACTCCACC
1 ACCAGTATAGGAAGACAAGATCT-ATTTCTTTGATCTACTCCA-C
* *
1166 ACCAGTATGGGGAGACAAGATCTATTTCTTTGATCTACTCCAC
1 ACCAGTATAGGAAGACAAGATCTATTTCTTTGATCTACTCCAC
* * *
1209 GCCAGTACATGAAGACAAGATCT
1 ACCAGTATAGGAAGACAAGATCT
1232 GCTTTTACAA
Statistics
Matches: 88, Mismatches: 21, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
43 19 0.22
44 49 0.56
45 20 0.23
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (43 bp):
ACCAGTATAGGAAGACAAGATCTATTTCTTTGATCTACTCCAC
Found at i:1228 original size:43 final size:44
Alignment explanation
Indices: 1104--1232 Score: 152
Period size: 44 Copynumber: 2.9 Consensus size: 44
1094 GGACCTACTA
* * *
1104 TCTTTGATCTACTTCACACCAGTATATGAAGACACGATCTGTTT
1 TCTTTGATCTACTCCACACCAGTATATGAAGACAAGATCTGATT
* * ** *
1148 TCTTCGACCTACTCCACCACCAGTATGGGGAGACAAGATCT-ATT
1 TCTTTGATCTACTCCA-CACCAGTATATGAAGACAAGATCTGATT
* *
1192 TCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATCTG
1 TCTTTGATCTACTCCACACCAGTATATGAAGACAAGATCTG
1233 CTTTTACAAT
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
43 19 0.28
44 29 0.43
45 20 0.29
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (44 bp):
TCTTTGATCTACTCCACACCAGTATATGAAGACAAGATCTGATT
Found at i:1474 original size:89 final size:89
Alignment explanation
Indices: 1061--1674 Score: 466
Period size: 89 Copynumber: 6.9 Consensus size: 89
1051 AATATGTATA
* * * * * * ** *
1061 TTCGATCCACTTCGCTACCAATATAGGAAGACAGGACCTACTATCTTTGATCTACTTCACACCAG
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAG
* *
1126 TATATGAAGACACGATCTGTTTTC
66 TACATGAAGACAAGATCTGTTTTC
* * * * * * *
1150 TTCGACCTACTCCACCACCAGTATGGGGAGACAAGATCT-ATTTCTTTGATCTACTCCACGCCAG
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAG
1214 TACATGAAGACAAGATCTGCTTTTAC
66 TACATGAAGACAAGATCTG-TTTT-C
* * * * * ** * *
1240 AATCTATTCCACTGCTG-C-CCAG---GGAGATAGA-AATA-CTGG---CTTCAATGTACTCCAC
1 -TTCGA-TCTACTTC-GCCACCAGTATGG-GA-AGACAAGATCTGGTATCTTTGATCTACTTCAC
** ** * * * ***
1295 TGTAACCACGAGGAGGTA-AA-ATCAGCCATC
61 -GCCAGTAC-ATGAAG-ACAAGATCTGTTTTC
* ** * * * **
1325 TTCGATCTGCTTCGCTGTCTA-TATAGGAAGGCAAGATCTGCCATCTTTGATCTACTTCACGCCA
1 TTCGATCTACTTCGC-CACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCA
*
1389 GTACATGAAGACAAGATCTATTTTC
65 GTACATGAAGACAAGATCTGTTTTC
*
1414 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTAATCTACTTCACGCCAG
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAG
* *
1479 TACATGAAGATAATATCTGTTTTC
66 TACATGAAGACAAGATCTGTTTTC
** * * * * * * * *
1503 TTTTATCTACTCCACCACTAGTATGGGGAGCCAAGATCT-GTTTCTTTGATCTACCTCACACCAG
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAG
1567 TACATGAAGACAAGATCTGTTTTC
66 TACATGAAGACAAGATCTGTTTTC
* *
1591 TTCGATCTACTTCGCCACCAGTATGGGAAAACAAGATCTGTTATCTTTGATCTACTTCACGCCAG
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAG
*
1656 CACATGAAGACAAGATCTG
66 TACATGAAGACAAGATCTG
1675 CTGCTTTTCA
Statistics
Matches: 397, Mismatches: 102, Indels: 52
0.72 0.19 0.09
Matches are distributed among these distances:
82 1 0.00
83 5 0.01
84 3 0.01
85 5 0.01
86 19 0.05
87 13 0.03
88 130 0.33
89 192 0.48
90 16 0.04
91 7 0.02
92 6 0.02
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (89 bp):
TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAG
TACATGAAGACAAGATCTGTTTTC
Found at i:1515 original size:353 final size:351
Alignment explanation
Indices: 867--1589 Score: 848
Period size: 353 Copynumber: 2.1 Consensus size: 351
857 ACCAGTATGG
* * * * *
867 GAAGACAAGATCTGCTTTTTCAATCGATTCCACTGCCGACCGGGGAGGTAGAATTACTAGCTTTA
1 GAAGACAAGATCTGCTTTTACAATCGATTCCACTGCCGACCAGGGAGATAGAAATACTAGCTTCA
* *
932 ATATACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTA
66 ATATACTCCACTGCAAC-TCAGGGAGGTAAAATCAGCCATCTTCGATCTGCTCCACTACTGATTA
* * * ** * *
997 GGGAGGCAAAATCTGTAATCTTCAATCTACTTTGCCGCCGGTATGGGGAGATAAAATATGTATAT
130 GGAAGGCAAAATCTGCAATCTTCAATCTACTTTGCCGCCAGTACAGGAAGACAAAATATGTATAT
* * *
1062 TCGATCCACTTCGCTACCAATATAGGAAGACAGGACCTACTATCTTTGATCTACTTCACACCAGT
195 TCGATCCACTTCGCCACCAATATAGGAAGACAAGACCTACTATCTTTAATCTACTTCACACCAGT
* *
1127 ATATGAAGACACGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGGAGACAAGATCTATT
260 ACATGAAGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGGAGACAAGATCTATT
*
1192 TCTTTGATCTA-CTCCACGCCAGTACAT
325 TCTTTGATCTACCT-CACACCAGTACAT
* * * *
1219 GAAGACAAGATCTGCTTTTACAATCTATTCCACTGCTGCCCAGGGAGATAGAAATACTGGCTTCA
1 GAAGACAAGATCTGCTTTTACAATCGATTCCACTGCCGACCAGGGAGATAGAAATACTAGCTTCA
* * * * *
1284 ATGTACTCCACTGTAAC-CACGAGGAGGTAAAATCAGCCATCTTCGATCTGCTTCGCTGTCT-AT
66 ATATACTCCACTGCAACTCA-G-GGAGGTAAAATCAGCCATCTTCGATCTGCTCCACT-ACTGAT
* * ** * *
1347 ATAGGAAGGCAAGATCTGCCATCTTTGATCTAC-TT-CACGCCAGTACATGAAGACAAGATCTAT
128 -TAGGAAGGCAAAATCTGCAATCTTCAATCTACTTTGC-CGCCAGTACAGGAAGACAA-A-ATAT
* * * * * * **
1410 -TTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTAATCTACTTCAC
189 GTATATTCGATCCACTTCGCCACCAATATAGGAAGACAAGACCTACTATCTTTAATCTACTTCAC
* * * ** * * *
1474 GCCAGTACATGAAGATAATATCTGTTTTCTTTTATCTACTCCACCACTAGTATGGGGAGCCAAGA
254 ACCAGTACATGAAGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGGAGACAAGA
*
1539 TCTGTTTCTTTGATCTACCTCACACCAGTACAT
319 TCTATTTCTTTGATCTACCTCACACCAGTACAT
1572 GAAGACAAGATCTG-TTTT
1 GAAGACAAGATCTGCTTTT
1590 CTTCGATCTA
Statistics
Matches: 311, Mismatches: 52, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
350 2 0.01
351 2 0.01
352 123 0.40
353 179 0.58
354 5 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (351 bp):
GAAGACAAGATCTGCTTTTACAATCGATTCCACTGCCGACCAGGGAGATAGAAATACTAGCTTCA
ATATACTCCACTGCAACTCAGGGAGGTAAAATCAGCCATCTTCGATCTGCTCCACTACTGATTAG
GAAGGCAAAATCTGCAATCTTCAATCTACTTTGCCGCCAGTACAGGAAGACAAAATATGTATATT
CGATCCACTTCGCCACCAATATAGGAAGACAAGACCTACTATCTTTAATCTACTTCACACCAGTA
CATGAAGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGGAGACAAGATCTATTT
CTTTGATCTACCTCACACCAGTACAT
Found at i:1674 original size:44 final size:44
Alignment explanation
Indices: 1351--1674 Score: 292
Period size: 44 Copynumber: 7.3 Consensus size: 44
1341 GTCTATATAG
* **
1351 GAAGGCAAGATCTGCCATCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACAT
* * * * * ***
1395 GAAGACAAGATCTATTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGTTATCTTTGATCTACTTC-ACGCCAGTACAT
* *
1440 GAAGACAAGATCTGGTATCTTTAATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACAT
* * * * * ***
1484 GAAGATAATATCTGTTTTCTTTTATCTACTCCAC-CACTAGTATGG
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGC-C-AGTACAT
* * * *
1529 GGAGCCAAGATCTGTT-TCTTTGATCTACCTCACACCAGTACAT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACAT
* * * * ***
1572 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGTTATCTTTGATCTACTTC-ACGCCAGTACAT
* *
1617 GAAAACAAGATCTGTTATCTTTGATCTACTTCACGCCAGCACAT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACAT
1661 GAAGACAAGATCTG
1 GAAGACAAGATCTG
1675 CTGCTTTTCA
Statistics
Matches: 216, Mismatches: 58, Indels: 12
0.76 0.20 0.04
Matches are distributed among these distances:
43 19 0.09
44 109 0.50
45 88 0.41
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (44 bp):
GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACAT
Found at i:3045 original size:57 final size:55
Alignment explanation
Indices: 2932--3046 Score: 140
Period size: 57 Copynumber: 2.1 Consensus size: 55
2922 TTAGCCTCTC
* * * * ***
2932 TTTTTTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTCTCTTTTTT
1 TTTTTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACCTTT
*
2987 TTTTCTTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTCCCACCTTT
1 TTTT-TTTTTTTT-ACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACCTTT
3044 TTT
1 TTT
3047 AAGCAGAGTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
55 4 0.08
56 8 0.16
57 38 0.76
ACGTcount: A:0.10, C:0.24, G:0.14, T:0.51
Consensus pattern (55 bp):
TTTTTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACCTTT
Found at i:5772 original size:19 final size:19
Alignment explanation
Indices: 5732--5774 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5722 ATAATCTTTG
* *
5732 ATGCATATGATGTAATGAA
1 ATGCAAATGATGAAATGAA
5751 ATGCAAATGCATGAAATG-A
1 ATGCAAATG-ATGAAATGAA
5770 ATGCA
1 ATGCA
5775 TAAAGAGACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (19 bp):
ATGCAAATGATGAAATGAA
Found at i:8163 original size:12 final size:12
Alignment explanation
Indices: 8146--8170 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8136 ATGAATGAAT
8146 ATAGAAATAATA
1 ATAGAAATAATA
8158 ATAGAAATAATA
1 ATAGAAATAATA
8170 A
1 A
8171 CAAACTAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
ATAGAAATAATA
Done.